Abstract：The Tibetan chicken (Gallus gallus domesticus), a chicken breed endemic to Tibetan Plateau, has adapted to the hypoxic, high-altitude environment over a thousand years. The study on the genetic diversity of the Tibetan chicken is of great significance for genetic conservation and inbreeding programs. In this study, 4 haplotypes were identified based on D-loop sequencing in Tibetan chicken (n=40), and each representative of 4 haplotypes were selected for total mitochondrial genome sequencing and analyzed together with published mitochondrial genome data of red jungle fowl. Four haplotypes belonged to 3 previously published clades, i.e., Clade A, clade B and clade E. Based on D-loop sequencing data, the average haplotype diversity and nucleotide diversity were 0.658±0.065 and 0.004 42±0.000 94, respectively. The mitochondrial genome of Tibetan chicken is 16 785 bp in size, consisting of 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes and 1 non-coding control region. There were 7 overlapping genes and 17 intergenic regions. The phylogenetic tree had different cluster branching based on D-loop sequences and the mitochondrial genome. The results indicated that Tibetan chicken populations in this study have relatively low nucleotide and haplotype diversity and likely share multiple maternal lineages. The D-loop sequence has limited power for the resolution of phylogenetic relationships in comparison with the complete mitochondrial genome. The results of the current study can be used as baseline genetic information for genetic conservation program and in breeding.
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